create_tool: stamp the data manager conf id the caller already hands us

Shed-installed data managers load their tool at install time, before
shed_data_manager_conf.xml exists — the self-healed entry carries
data_manager_id=None, materialise never restores the conf id, and
DataManagerTool.exec_after_process fails with 'Invalid data manager
(<guid>)' at job finish (all six data-manager integration tests).

DataManager._load_tool already passes data_manager_id through
load_hidden_tool; create_tool now stamps it onto the resolved entry and
persists it, so job handlers materialising from the shared index
resolve the registry correctly.

lib/galaxy/tools/lazy_toolbox.py

@@ -791,6 +791,22 @@ class LazyToolBox(ToolBox):
                 "or, for a new Galaxy-internal lib tool, add it to "
                 "galaxy.tools.special_tools.hidden_lib_tool_paths()."
             )
+        data_manager_id = kwds.get("data_manager_id")
+        if data_manager_id and not entry.data_manager_id:
+            # ``DataManager._load_tool`` hands the ``<data_manager id>`` conf
+            # id through ``load_hidden_tool``. Entries minted before any data
+            # manager conf covered this tool (install-time self-heal) don't
+            # carry it, and the materialise path must restore it or
+            # ``DataManagerTool.exec_after_process`` falls back to the tool
+            # id and misses the registry. Persist so job-handler processes
+            # materialising from the shared index see it too.
+            entry.data_manager_id = data_manager_id
+            if self._store is not None:
+                try:
+                    self._store.update_index_entry(entry)
+                    self._store.commit()
+                except Exception as e:
+                    log.warning("Persisting data_manager_id for %s raised: %s", entry.id, e)
         # LazyTool is duck-typed against Tool — the eager pipeline (audited
         # in plans/witty-drifting-clock.md) only consults attributes the
         # stub forwards from ToolIndexEntry, with mutations stored on

test/unit/app/tools/test_lazy_tool.py

@@ -356,6 +356,16 @@ def test_create_tool_populates_adhoc_for_existing_file(tmp_path, monkeypatch):
     box._store.invalidate_index_cache.assert_called()
 
 
+def test_create_tool_stamps_data_manager_conf_id_on_entry():
+    box = _seam_box()
+    e = _entry(id="dm_tool", tool_type="manage_data")
+    box._tool_index.entries["dm_tool"] = e
+    tool = box.create_tool(config_file=None, guid="dm_tool", data_manager_id="test_data_manager")
+    assert isinstance(tool, LazyTool)
+    assert e.data_manager_id == "test_data_manager"
+    box._store.update_index_entry.assert_called_once_with(e)
+
+
 def test_create_tool_raises_on_index_miss():
     # The populator owns the index — including the Galaxy-internal lib
     # tools listed in ``galaxy.tools.special_tools.hidden_lib_tool_paths``.